def generate_referenced_species_database(protein_id, referenced_species):
'''
Creates a database for a referenced species and protein, using formatdb
@param protein_id
@param referenced_species
'''
logger = Logger.Instance()
alignment_logger = logger.get_logger('alignment')
command_generator = CommandGenerator()
crawler = DirectoryCrawler()
exon_container = ExonContainer.Instance()
input_exons = exon_container.get((protein_id, referenced_species, "ensembl"))
#source_exon_file = "{0}/{1}.fa".format(crawler.get_exon_ensembl_path(protein_id), referenced_species)
input_db_file = "{0}/{1}.fa".format(crawler.get_database_path(protein_id), referenced_species)
sequence_type = "Nucleotide"
input_exons.export_coding_exons_to_fasta(input_db_file)
command = command_generator.generate_formatdb_command(input_db_file, sequence_type)
command_return = Popen(command, shell=True, stdin=PIPE, stdout=PIPE, stderr=STDOUT, close_fds=True)
output = command_return.stdout.read()
if output != "":
#LOGGING
alignment_logger.warning("{0}, {1}, REF SPECIES DB, {2}".format(protein_id, referenced_species.strip(), output.strip()))
return False
return True
